Molecular dynamics simulations: bring biomolecular structures alive on a computer

Shunzhou Wan; Peter V. Coveney; Darren R. Flower

doi:10.1007/978-1-60327-118-9_24

Molecular dynamics simulations: bring biomolecular structures alive on a computer

Shunzhou Wan
, Peter V. Coveney
, Darren R. Flower

University College London
University of Oxford

Research output: Chapter in Book/Published conference output › Chapter (peer-reviewed) › peer-review

2 Citations (Scopus)

Abstract

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.

Original language	English
Title of host publication	Immunoinformatics
Subtitle of host publication	predicting immunogenicity in silico
Editors	Darren R. Flowers
Place of Publication	Totowa, NJ (US)
Publisher	Humana Press
Pages	321-339
Number of pages	19
ISBN (Electronic)	978-1-60327-118-9
ISBN (Print)	978-1-58829-699-3
DOIs	https://doi.org/10.1007/978-1-60327-118-9_24
Publication status	Published - 16 Jul 2007

Publication series

Name	Methods in molecular biology™
Publisher	Humana Press
Volume	409
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

molecular dynamics simulation
visualization
major histocompatibility complex

Access to Document

10.1007/978-1-60327-118-9_24

Cite this

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Molecular dynamics simulations: bring biomolecular structures alive on a computer. / Wan, Shunzhou; Coveney, Peter V.; Flower, Darren R.
Immunoinformatics: predicting immunogenicity in silico. ed. / Darren R. Flowers. Totowa, NJ (US): Humana Press, 2007. p. 321-339 (Methods in molecular biology™; Vol. 409).

Research output: Chapter in Book/Published conference output › Chapter (peer-reviewed) › peer-review

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AU - Coveney, Peter V.

AU - Flower, Darren R.

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KW - major histocompatibility complex

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M3 - Chapter (peer-reviewed)

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Molecular dynamics simulations: bring biomolecular structures alive on a computer

Abstract

Publication series

UN SDGs

Keywords

Access to Document

Other files and links

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Immunoinformatics: predicting immunogenicity in silico

Immunoinformatics and the in silico prediction of immunogenicity: an introduction

In silico prediction of peptide-MHC binding affinity using SVRMHC

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